Hurricanes damage estuaries and coastal habitats the most, as well as many other habitats. The strong winds the hurricane brings can defoiliate forest areas, clearing away leaves and causing dramatic changes. The heavy rainfall and the storm surge can also cause floods. Still, hurricanes can kill animals living in the affected area immediately or the changes or the animals habitat caused by the hurricane will kill the animal. Along with that, there may be food shortage, another contributing factor to the death of an animal, due to the fact that the prey has died.

Sediment erosion and deposition affects coral reefs and oyster beds. Also, hurricanes bring in saltwater to the freshwater lakes, which can harm the aquatic animals there. Often, floodwater (water overflowing as the result of a flood) is contaminated by heavy metals, pesticides, ammonia, phosphate and untreated water sewage. These substances can cause a degration of water quality. This also may cause a decrease in dissolved oxygen which harm organisms if there is not enough.

Storm surge causes sediments to shift; barrier islands may be eroded below sea level or shifted. Mangrove forests, which are home to some birds, may also be destroyed. The fallen trees could be fuel for a forest fire. Salt water makes some habitats unsuitable for some animals to live and sea grass beds are destroyed. Sea grass beds are very much needed for feeding and nesting.